Part 1: Call to Arms
I think the first part should focus on the real start of hostilities with the mining of the entrance of the Bajoran Wormhole. A new Deep Space 9 card is warranted with updated stats, Deep Space 9 and Terrok Nor. I think Alpha Quadrant versions of Weyoun, the Founder Leader and even Gamma Jem'Hadar are warranted, including their ships, along with dual and personnel and ships. Cards would be from episodes where the station is occupied (Call to Arms) up to the point where it is retaken (Sacrifice of Angels). Rom, Leeta, Kira, Odo, Ziyal, Morn and Quark as infiltrators, and some new cards to help them wreak havoc. We'd finally get a Salvaged Attack Ship, and hopefully an objective to recover it along with an objective to blow up a Jem'Hadar station.
Would focus on the Klingons and Romulans part in the war. More cards from "In the Pale Moonlight", Chancellor Martok, ships for and that are either remade into logo cards or entirely new spins on them. Fantasy cards to fill in the details on the occupation of Betazed could be alot of fun since 2-E got some.
Would focus on the Breen, the Cardassian resistance movement and the last episodes featuring the Dominion War. The Breen need a lot of love in the form or ships and personnel. Shipyard cards could be introduced as well, and objectives to destroy them. Battle and occupation related Objectives and Incidents would hopefully be added threw out the block, along with new tactics with the DS9 logo. A USS Defiant persona of USS Sao Paulo is also merited, along with a Dominion version of the USS Defiant from when it was captured (two different occasions I might add).
This was supposed to be more detailed, but it got late really quickly, lol. Time for bed, I might edit this with more ideas later. But in the meantime, what are your ideas?